Scale at the interface of spatial and social ecology

Animals simultaneously navigate spatial and social environments, and their decision-making with respect to those environments constitutes their spatial (e.g. habitat selection) and social (e.g. conspecific associations) phenotypes. The spatial-social interface is a recently introduced conceptual framework linking these components of spatial and social ecology. The spatial-social interface is inherently scale-dependent, yet it has not been integrated with the rich body of literature on ecological scale. Here, we develop a conceptual connection between the spatial-social interface and ecological scale. We propose three key innovations that incrementally build upon each other. First, the use-availability framework that underpins a large body of literature in behavioural ecology can be used in analogy to the phenotype-environment nomenclature and is transferable across the spatial and social realms. Second, both spatial and social phenotypes are hierarchical, with nested components that are linked via constraints-from the top down-or emergent properties-from the bottom up. Finally, in both the spatial and social realms, the definitions of environment and phenotype depend on the focal scale of inquiry. These conceptual innovations cast our understanding of the relationships between social and spatial dimensions of animal ecology in a new light, allowing a more holistic understanding and clearer hypothesis development for animal behaviour. This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.

Understanding Trophic Interactions in a Warming World by Bridging Foraging Ecology and Biomechanics with Network Science

Climate change will disrupt biological processes at every scale. Ecosystem functions and services vital to ecological resilience are set to shift, with consequences for how we manage land, natural resources, and food systems. Increasing temperatures cause morphological shifts, with concomitant implications for biomechanical performance metrics crucial to trophic interactions. Biomechanical performance, such as maximum bite force or running speed, determines the breadth of resources accessible to consumers, the outcome of interspecific interactions, and thus the structure of ecological networks. Climate change-induced impacts to ecosystem services and resilience are therefore on the horizon, mediated by disruptions of biomechanical performance and, consequently, trophic interactions across whole ecosystems. Here, we argue that there is an urgent need to investigate the complex interactions between climate change, biomechanical traits, and foraging ecology to help predict changes to ecological networks and ecosystem functioning. We discuss how these seemingly disparate disciplines can be connected through network science. Using an ant-plant network as an example, we illustrate how different data types could be integrated to investigate the interaction between warming, bite force, and trophic interactions, and discuss what such an integration will achieve. It is our hope that this integrative framework will help to identify a viable means to elucidate previously intractable impacts of climate change, with effective predictive potential to guide management and mitigation.

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils

Expanding and intensifying agriculture has led to a loss of soil carbon. As agroecosystems cover over 40% of Earth's land surface, they must be part of the solution put in action to mitigate climate change. Development of efficient management practices to maximize soil carbon retention is currently limited, in part, by a poor understanding of how plants, which input carbon to soil, and microbes, which determine its fate there, interact. Here we implement a diversity gradient by intercropping undersown species with barley in a large field trial, ranging from one to eight undersown species. We find that increasing plant diversity strengthens positive associations within the rhizosphere soil microbial community in relation to negative associations. These associations, in turn, enhance community carbon use efficiency. Jointly, our results highlight how increasing plant diversity in agriculture can be used as a management strategy to enhance carbon retention potential in agricultural soils.

Ecological networks in savannas reflect different levels of hydric stress in adjacent palm swamp forest ecosystems

Palm swamp forests are wetland ecosystems typical of the Brazilian Cerrado, which in recent decades have undergone intense changes due to land use alterations and climate change. As a result of these disturbances, many palm swamps have been experiencing significant drying, which can also affect adjacent vegetation. In the present study, we evaluated whether the drying of palm swamps affects the structure of plant-herbivore networks located in adjacent savanna areas in Brazil. Our results show that savanna areas adjacent to dry zones of palm swamps have fewer interactions, fewer interacting species, and a less specialized topology, which corroborates our expectations. Our findings indicate that the drying of palm swamps also has propagated impacts on adjacent savanna vegetation, impairing more specialized interactions in these environments. On the other hand, contrary to expectations, plant-herbivore networks in dry zones displayed higher modularity, lower nestedness and lower robustness than those in wet zones, suggesting that in dry environments, species tend to compartmentalize their interactions, even with lower interaction specialization. This is the first study to investigate the impacts of environmental drying on the structure of plant-herbivore networks in tropical ecosystems, highlighting the complexity of these effects and their differential impact on specialized and generalized interactions. Understanding these dynamics is crucial for developing effective conservation and management strategies in the face of ongoing environmental changes.

On formal limitations of causal ecological networks

Causal multivariate time-series analysis, combined with network theory, provide a powerful tool for studying complex ecological interactions. However, these methods have limitations often underestimated when used in graphical modelling of ecological systems. In this opinion article, I examine the relationship between formal logic methods used to describe causal networks and their inherent statistical and epistemological limitations. I argue that while these methods offer valuable insights, they are restricted by axiomatic assumptions, statistical constraints and the incompleteness of our knowledge. To prove that, I first consider causal networks as formal systems, define causality and formalize their axioms in terms of modal logic and use ecological counterexamples to question the axioms. I also highlight the statistical limitations when using multivariate time-series analysis and Granger causality to develop ecological networks, including the potential for spurious correlations among other data characteristics. Finally, I draw upon Gödel's incompleteness theorems to highlight the inherent limits of fully understanding complex networks as formal systems and conclude that causal ecological networks are subject to initial rules and data characteristics and, as any formal system, will never fully capture the intricate complexities of the systems they represent. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

A novel hierarchical network-based approach to unveil the complexity of functional microbial genome

Biological networks serve a crucial role in elucidating intricate biological processes. While interspecies environmental interactions have been extensively studied, the exploration of gene interactions within species, particularly among individual microorganisms, is less developed. The increasing amount of microbiome genomic data necessitates a more nuanced analysis of microbial genome structures and functions. In this context, we introduce a complex structure using higher-order network theory, "Solid Motif Structures (SMS)", via a hierarchical biological network analysis of genomes within the same genus, effectively linking microbial genome structure with its function. Leveraging 162 high-quality genomes of Microcystis, a key freshwater cyanobacterium within microbial ecosystems, we established a genome structure network. Employing deep learning techniques, such as adaptive graph encoder, we uncovered 27 critical functional subnetworks and their associated SMSs. Incorporating metagenomic data from seven geographically distinct lakes, we conducted an investigation into Microcystis' functional stability under varying environmental conditions, unveiling unique functional interaction models for each lake. Our work compiles these insights into an extensive resource repository, providing novel perspectives on the functional dynamics within Microcystis. This research offers a hierarchical network analysis framework for understanding interactions between microbial genome structures and functions within the same genus.

Morphological traits explain the individual position within resource-consumer networks of a Neotropical marsupial

Knowledge regarding the influence of individual traits on interaction patterns in nature can help understand the topological role of individuals within a network of intrapopulation interactions. We tested hypotheses on the relationships between individuals' positions within networks (specialization and centrality) of 4 populations of the mouse opossum Gracilinanus agilis and their traits (i.e., body length, body condition, tail length relative to body length, sex, reproductive condition, and botfly parasitism) and also seasonal effects in the Brazilian savanna. Individuals with lower body length, better body condition, and relatively shorter tail were more specialized (i.e., less connected within the network). Individuals were also more specialized and less connected during the warm-wet season. The relationship between individuals' position in the network and body traits, however, was independent of season. We propose that specialization may arise not only as a result of preferred feeding strategies by more capable individuals (i.e., those with better body condition and potentially prone to defend and access high-quality food resources) but also because of morphological constraints. Smaller/younger individuals (consequently with less experience in foraging) and short-tailed individuals (less skilled to explore the vertical strata of the vegetation) would feed only on a subset of the available food resources and consequently become more specialized. Moreover, individuals are more specialized during the warm-wet season because of high competition (population-dense period) and higher ecological opportunities (resource-rich period). Therefore, our study reveals the relevance of individual traits in shaping interaction patterns and specialization in populations.

Biodiversity in changing environments: An external-driver internal-topology framework to guide intervention

Accompanying the climate crisis is the more enigmatic biodiversity crisis. Rapid reorganization of biodiversity due to global environmental change has defied prediction and tested the basic tenets of conservation and restoration. Conceptual and practical innovation is needed to support decision making in the face of these unprecedented shifts. Critical questions include: How can we generalize biodiversity change at the community level? When are systems able to reorganize and maintain integrity, and when does abiotic change result in collapse or restructuring? How does this understanding provide a template to guide when and how to intervene in conservation and restoration? To this end, we frame changes in community organization as the modulation of external abiotic drivers on the internal topology of species interactions, using plant-plant interactions in terrestrial communities as a starting point. We then explore how this framing can help translate available data on species abundance and trait distributions to corresponding decisions in management. Given the expectation that community response and reorganization are highly complex, the external-driver internal-topology (EDIT) framework offers a way to capture general patterns of biodiversity that can help guide resilience and adaptation in changing environments.

The persistence of bipartite ecological communities with Lotka-Volterra dynamics

The assembly and persistence of ecological communities can be understood as the result of the interaction and migration of species. Here we study a single community subject to migration from a species pool in which inter-specific interactions are organised according to a bipartite network. Considering the dynamics of species abundances to be governed by generalised Lotka-Volterra equations, we extend work on unipartite networks to we derive exact results for the phase diagram of this model. Focusing on antagonistic interactions, we describe factors that influence the persistence of the two guilds, locate transitions to multiple-attractor and unbounded phases, as well as identifying a region of parameter space in which consumers are essentially absent in the local community.

Latitudinal specificity of plant-avian frugivore interactions

Broad-scale assessments of plant-frugivore interactions indicate the existence of a latitudinal gradient in interaction specialization. The specificity (i.e. the similarity of the interacting partners) of plant-frugivore interactions could also change latitudinally given that differences in resource availability could favour species to become more or less specific in their interactions across latitudes. Species occurring in the tropics could be more taxonomically, phylogenetically and functionally specific in their interactions because of a wide range of resources that are constantly available in these regions that would allow these species to become more specialized in their resource usage. We used a data set on plant-avian frugivore interactions spanning a wide latitudinal range to examine these predictions, and we evaluated the relationship between latitude and taxonomic, phylogenetic and functional specificity of plant and frugivore interactions. These relationships were assessed using data on population interactions (population level), species means (species level) and community means (community level). We found that the specificity of plant-frugivore interactions is generally not different from null models. Although statistically significant relationships were often observed between latitude and the specificity of plant-frugivore interactions, the direction of these relationships was variable and they also were generally weak and had low explanatory power. These results were consistent across the three specificity measures and levels of organization, suggesting that there might be an interplay between different mechanisms driving the interactions between plants and frugivores across latitudes.

Network Models of BACE-1 Inhibitors: Exploring Structural and Biochemical Relationships

This study investigates the clustering patterns of human β-secretase 1 (BACE-1) inhibitors using complex network methodologies based on various distance functions, including Euclidean, Tanimoto, Hamming, and Levenshtein distances. Molecular descriptor vectors such as molecular mass, Merck Molecular Force Field (MMFF) energy, Crippen partition coefficient (ClogP), Crippen molar refractivity (MR), eccentricity, Kappa indices, Synthetic Accessibility Score, Topological Polar Surface Area (TPSA), and 2D/3D autocorrelation entropies are employed to capture the diverse properties of these inhibitors. The Euclidean distance network demonstrates the most reliable clustering results, with strong agreement metrics and minimal information loss, indicating its robustness in capturing essential structural and physicochemical properties. Tanimoto and Hamming distance networks yield valuable clustering outcomes, albeit with moderate performance, while the Levenshtein distance network shows significant discrepancies. The analysis of eigenvector centrality across different networks identifies key inhibitors acting as hubs, which are likely critical in biochemical pathways. Community detection results highlight distinct clustering patterns, with well-defined communities providing insights into the functional and structural groupings of BACE-1 inhibitors. The study also conducts non-parametric tests, revealing significant differences in molecular descriptors, validating the clustering methodology. Despite its limitations, including reliance on specific descriptors and computational complexity, this study offers a comprehensive framework for understanding molecular interactions and guiding therapeutic interventions. Future research could integrate additional descriptors, advanced machine learning techniques, and dynamic network analysis to enhance clustering accuracy and applicability.

Evolutionary Game Dynamics with Environmental Feedback in a Network with Two Communities

Recent developments of eco-evolutionary models have shown that evolving feedbacks between behavioral strategies and the environment of game interactions, leading to changes in the underlying payoff matrix, can impact the underlying population dynamics in various manners. We propose and analyze an eco-evolutionary game dynamics model on a network with two communities such that players interact with other players in the same community and those in the opposite community at different rates. In our model, we consider two-person matrix games with pairwise interactions occurring on individual edges and assume that the environmental state depends on edges rather than on nodes or being globally shared in the population. We analytically determine the equilibria and their stability under a symmetric population structure assumption, and we also numerically study the replicator dynamics of the general model. The model shows rich dynamical behavior, such as multiple transcritical bifurcations, multistability, and anti-synchronous oscillations. Our work offers insights into understanding how the presence of community structure impacts the eco-evolutionary dynamics within and between niches.

The propagation of disturbances in ecological networks

Despite the development of network science, we lack clear heuristics for how far different disturbance types propagate within and across species interaction networks. We discuss the mechanisms of disturbance propagation in ecological networks, and propose that disturbances can be categorized into structural, functional, and transmission types according to their spread and effect on network structure and functioning. We describe the properties of species and their interaction networks and metanetworks that determine the indirect, spatial, and temporal extent of propagation. We argue that the sampling scale of ecological studies may have impeded predictions regarding the rate and extent that a disturbance spreads, and discuss directions to help ecologists to move towards a predictive understanding of the propagation of impacts across interacting communities and ecosystems.

Properties of vertebrate predator-prey networks in the high Arctic

Predation is an important ecological process that can significantly impact the maintenance of ecosystem services. In arctic environments, the relative ecological importance of predation is thought to be increasing due to climate change, partly because of increased productivity with rising temperatures. Therefore, understanding predator-prey interactions in arctic ecosystems is vital for the sustainable management of these northern regions. Network theory provides a framework for quantifying the structures of ecological interactions. In this study, we use dietary observations on mammalian and avian predators in a high arctic region, including isolated peninsulas on Ellesmere Island and north Greenland, to construct bipartite trophic networks. We quantify the complexity, specialization, and nested as well as modular structures of these networks and also determine if these properties varied among the peninsulas. Mammal prey remains were the dominant diet item for all predators, but there was spatial variation in diet composition among peninsulas. The predator-prey networks were less complex, had more specialized interactions, and were more nested and more modular than random expectations. However, the networks displayed only moderate levels of modularity. Predator species had less specialized interactions with prey than prey had with predators. All network properties differed among the peninsulas, which highlights that ecosystems often show complex responses to environmental characteristics. We suggest that gaining knowledge about spatial variation in the characteristics of predator-prey interactions can enhance our ability to manage ecosystems exposed to environmental perturbations, particularly in high arctic environments subject to rapid environmental change.

Structural dynamics of plant-pollinator mutualistic networks

The discourse surrounding the structural organization of mutualistic interactions mostly revolves around modularity and nestedness. The former is known to enhance the stability of communities, while the latter is related to their feasibility, albeit compromising the stability. However, it has recently been shown that the joint emergence of these structures poses challenges that can eventually lead to limitations in the dynamic properties of mutualistic communities. We hypothesize that considering compound arrangements-modules with internal nested organization-can offer valuable insights in this debate. We analyze the temporal structural dynamics of 20 plant-pollinator interaction networks and observe large structural variability throughout the year. Compound structures are particularly prevalent during the peak of the pollination season, often coexisting with nested and modular arrangements in varying degrees. Motivated by these empirical findings, we synthetically investigate the dynamics of the structural patterns across two control parameters-community size and connectance levels-mimicking the progression of the pollination season. Our analysis reveals contrasting impacts on the stability and feasibility of these mutualistic communities. We characterize the consistent relationship between network structure and stability, which follows a monotonic pattern. But, in terms of feasibility, we observe nonlinear relationships. Compound structures exhibit a favorable balance between stability and feasibility, particularly in mid-sized ecological communities, suggesting they may effectively navigate the simultaneous requirements of stability and feasibility. These findings may indicate that the assembly process of mutualistic communities is driven by a delicate balance among multiple properties, rather than the dominance of a single one.

Local and extensive fluctuations in sparsely interacting ecological communities

Ecological communities with many species can be classified into dynamical phases. In systems with all-to-all interactions, a phase where species abundances always reach a fixed point and a phase where they continuously fluctuate have been found. The dynamics when interactions are sparse, with each species interacting with only a few others, has remained largely unexplored. Here we study a system of sparse interactions, first when interactions are of constant strength and completely unidirectional, and then when adding variability and bidirectionality. We show that in this case a phase unique to the sparse setting appears in the phase diagram, where for the same control parameters different communities may reach either a fixed point or a state where the abundances of only a finite subset of species fluctuate, and we calculate the probability for each outcome. These fluctuating species are organized around short cycles in the interaction graph, and their abundances undergo large nonlinear fluctuations. We characterize the approach from this phase to a phase with extensively many fluctuating species, and show that the probability of fluctuations grows continuously to one as the transition is approached, and that the number of fluctuating species diverges. This is qualitatively distinct from the transition to extensive fluctuations coming from a fixed point phase, which is marked by a loss of linear stability. The differences are traced back to the emergent binary character of the dynamics when far from short cycles.

Geographic differences in body size distributions underlie food web connectance of tropical forest mammals

Understanding variation in food web structure over large spatial scales is an emerging research agenda in food web ecology. The density of predator-prey links in a food web (i.e., connectance) is a key measure of network complexity that describes the mean proportional dietary breadth of species within a food web. Connectance is a critical component of food web robustness to species loss: food webs with lower connectance have been shown to be more susceptible to secondary extinctions. Identifying geographic variation in food web connectance and its drivers may provide insight into community robustness to species loss. We investigated the food web connectance of ground-dwelling tropical forest mammal communities in multiple biogeographic regions to test for differences among regions in food web connectance and to test three potential drivers: primary productivity, contemporary anthropogenic pressure, and variation in mammal body mass distributions reflective of historical extinctions. Mammal communities from fifteen protected forests throughout the Neo-, Afro-, and Asian tropics were identified from systematic camera trap arrays. Predator-prey interaction data were collected from published literature, and we calculated connectance for each community as the number of observed predator-prey links relative to the number of possible predator-prey links. We used generalized linear models to test for differences among regions and to identify the site level characteristics that best predicted connectance. We found that mammal food web connectance varied significantly among continents and that body size range was the only significant predictor. More possible predator-prey links were observed in communities with smaller ranges in body size and therefore sites with smaller body size ranges had higher mean proportional dietary breadth. Specifically, mammal communities in the Neotropics and in Madagascar had significantly higher connectance than mammal communities in Africa. This geographic variation in contemporary mammalian food web structure may be the product of historical extinctions in the Late Quaternary, which led to greater losses of large-bodied species in the Neotropics and Madagascar thus contributing to higher average proportional dietary breadth among the remaining smaller bodied species in these regions.

Exploring interactions between parasites and their hosts in the Pantanal floodplain using an ecological network approach

The study of host-parasite interactions is essential to understand the role of each host species in the parasitic transmission cycles in a given community. The use of ecological network highlights the patterns of interactions between hosts and parasites, allowing us to evaluate the underlying structural features and epidemiological roles of different species within this context. Through network analysis, we aimed to understand the epidemiological roles of mammalian hosts species (n = 67) and their parasites (n = 257) in the Pantanal biome. Our analysis revealed a modular pattern within the network, characterized by 14 distinct modules, as well as nestedness patterns within these modules. Some key nodes, such as the multi-host parasites Trypanosoma cruzi and T. evansi, connect different modules and species. These central nodes showed us that various hosts species, including those with high local abundances, contribute to parasite maintenance. Ectoparasites, such as ticks and fleas, exhibit connections that reflect their roles as vectors of certain parasites. Overall, our findings contribute to a comprehensive understanding of the structure of host-parasite interactions in the Pantanal ecosystem, highlighting the importance of network analysis as a tool to identifying the main transmission routes and maintenance of parasites pathways. Such insights are valuable for parasitic disease control and prevention strategies and shed light on the broader complexities of ecological communities.

Probabilistic activity driven model of temporal simplicial networks and its application on higher-order dynamics

Network modeling characterizes the underlying principles of structural properties and is of vital significance for simulating dynamical processes in real world. However, bridging structure and dynamics is always challenging due to the multiple complexities in real systems. Here, through introducing the individual's activity rate and the possibility of group interaction, we propose a probabilistic activity-driven (PAD) model that could generate temporal higher-order networks with both power-law and high-clustering characteristics, which successfully links the two most critical structural features and a basic dynamical pattern in extensive complex systems. Surprisingly, the power-law exponents and the clustering coefficients of the aggregated PAD network could be tuned in a wide range by altering a set of model parameters. We further provide an approximation algorithm to select the proper parameters that can generate networks with given structural properties, the effectiveness of which is verified by fitting various real-world networks. Finally, we construct the co-evolution framework of the PAD model and higher-order contagion dynamics and derive the critical conditions for phase transition and bistable phenomenon using theoretical and numerical methods. Results show that tendency of participating in higher-order interactions can promote the emergence of bistability but delay the outbreak under heterogeneous activity rates. Our model provides a basic tool to reproduce complex structural properties and to study the widespread higher-order dynamics, which has great potential for applications across fields.

Using individual-based trait frequency distributions to forecast plant-pollinator network responses to environmental change

Determining how and why organisms interact is fundamental to understanding ecosystem responses to future environmental change. To assess the impact on plant-pollinator interactions, recent studies have examined how the effects of environmental change on individual interactions accumulate to generate species-level responses. Here, we review recent developments in using plant-pollinator networks of interacting individuals along with their functional traits, where individuals are nested within species nodes. We highlight how these individual-level, trait-based networks connect intraspecific trait variation (as frequency distributions of multiple traits) with dynamic responses within plant-pollinator communities. This approach can better explain interaction plasticity, and changes to interaction probabilities and network structure over spatiotemporal or other environmental gradients. We argue that only through appreciating such trait-based interaction plasticity can we accurately forecast the potential vulnerability of interactions to future environmental change. We follow this with general guidance on how future studies can collect and analyse high-resolution interaction and trait data, with the hope of improving predictions of future plant-pollinator network responses for targeted and effective conservation.

Lotka-Volterra model with Allee effect: equilibria, coexistence and size scaling of maximum and minimum abundance

The Lotka-Volterra competition model (LVCM) is a fundamental tool for ecology, widely used to represent complex communities. The Allee effect (AE) is a phenomenon in which there is a positive correlation between population density and fitness, at low population densities. However, the interplay between the LVCM and AE has been seldom analyzed in multispecies models. Here, we analyze the mathematical properties of the LVCM [Formula: see text] AE, investigating the coexistence of species interacting through neutral diffuse competition, their equilibria and stable points. Minimum viable population density arises as the threshold below which species go extinct, characteristic of strong Allee effects. Then, by imposing relationships of main parameters to body size, i.e. allometric scaling, we derive a general solution to the size-scaling maximum and minimum expected density under plausible scenarios. The scaling of maximum population density is consistent with the literature, but we also provide novel predictions on the scaling of the lower limit to population density, a critical value for conservation science. The resulting framework is general and yields results that increase our current understanding of how complex demographic processes can be linked to ubiquitous ecological patterns.

The role of phenotypic plasticity in shaping ecological networks

Plasticity-mediated changes in interaction dynamics and structure may scale up and affect the ecological network in which the plastic species are embedded. Despite their potential relevance for understanding the effects of plasticity on ecological communities, these effects have seldom been analysed. We argue here that, by boosting the magnitude of intra-individual phenotypic variation, plasticity may have three possible direct effects on the interactions that the plastic species maintains with other species in the community: may expand the interaction niche, may cause a shift from one interaction niche to another or may even cause the colonization of a new niche. The combined action of these three factors can scale to the community level and eventually expresses itself as a modification in the topology and functionality of the entire ecological network. We propose that this causal pathway can be more widespread than previously thought and may explain how interaction niches evolve quickly in response to rapid changes in environmental conditions. The implication of this idea is not solely eco-evolutionary but may also help to understand how ecological interactions rewire and evolve in response to global change.

Network and parasitological analyses reveal latitudinal gradient in bats-ectoparasitic fly interactions across the Neotropic

Ecological interactions between parasites and their hosts play a fundamental role in evolutionary processes. Selection pressures are exerted on parasites and their hosts, usually resulting in high levels of specificity. Such is the case of ectoparasitic bat-flies, but how large-scale spatial gradients affect the dynamics of their interactions with their bat hosts is still unknown. In the present study, we investigated interaction patterns between bats and their ectoparasitic flies (Streblidae and Nycteribiidae), both presenting their peak of diversity in the Neotropical region, along a latitudinal gradient. Using network analyses and parasitic indices, grounded on the latitudinal diversity gradient pattern, we evaluated how spatial gradients affect species interactions and parasitic indices at the biogeopraphic scale, with increasing species richness in interaction networks closer to the tropics, leading to increases in network modularity, size, and specialization, and to a decrease in nesting and connectivity. We conducted a literature review, focusing on studies done in the Neotropical region, and own data. We obtained a bat richness of 97 species parasitized by 128 species of ectoparasitic flies, distributed into 57 interaction networks between latitudes 29° S and 19° N in the Neotropic. Network metrics and parasitic indices varied along the latitudinal gradient, with changes in the richness of bats and their ectoparasitic flies and in the structure of their interactions; network specialization, modularity, and connectance increase with latitude, while network size decreases with latitude. Regions closer to the equator had higher parasite loads. Our results show that interaction network metrics present a latitudinal gradient and that such interactions, when observed at a local scale, hide variations that only become perceptible at larger scales. In this way, ectoparasites such as bat flies are not only influenced by the ecology and biology of their hosts, but also by other environmental factors acting directly on their distribution and survival.

metanetwork: A R package dedicated to handling and representing trophic metanetworks

Trophic networks describe interactions between species at a given location and time. Due to environmental changes, anthropogenic perturbations or sampling effects, trophic networks may vary in space and time. The collection of network time series or networks in different sites thus constitutes a metanetwork. We present here the R package metanetwork, which will ease the representation, the exploration and analysis of trophic metanetwork data sets that are increasingly available. Our main methodological advance consists in suitable layout algorithm for trophic networks, which is based on trophic levels and dimension reduction in a graph diffusion kernel. In particular, it highlights relevant features of trophic networks (trophic levels, energetic channels). In addition, we developed tools to handle, compare visually and quantitatively and aggregate those networks. Static and dynamic visualisation functions have been developed to represent large networks. We apply our package workflow to several trophic network data sets.

Modularity in host-parasite mixed networks: interaction configuration shifts based on human perturbation and parasitism form

Parasitism is an association based on host individual traits and environmental factors. The complexity of this type of interaction is often lost when studying species-by-species interaction networks. Here we analyze changes in modularity - a metric describing groups of nodes interacting much more frequently among themselves than they do with nodes of other modules, considering the host individual variation and the different forms of parasitism: ecto- and endo-parasitism. For this, we studied mixed networks: bipartite networks comprising host individuals and parasite species as two sets of nodes interacting with each other. We used a fish-parasite mixed network from a highly perturbed coastal river to understand how an anthropogenic perturbation gradient influences the modular structure of host-parasite networks. In addition, we tested how host individual traits drove module configuration within host-parasite mixed networks. Our results showed that different forms of parasitism respond differently to the environment: modularity in fish-ectoparasite networks increased with human perturbation, but modularity was not related to human perturbation in fish-endoparasite networks. In addition, mixed network modules were intrinsically related to individual variation, with host intensity of infection being the most important trait, regardless of the parasite's life form. The effect of total abundance over network structure indicates signs of changes in community equilibrium, with an increase in species with opportunistic behaviors. Module composition was also related to host fitness and body size, which were most predictive in more preserved and diverse river sections. Overall, our results indicate that host-parasite networks are sensitive to ecological gradients marked by human perturbation and that host individual fitness helps to determine network structure.

The turnover of plant-frugivore interactions along plant range expansion: consequences for natural colonization processes

Plant-animal mutualisms such as seed dispersal are key interactions for sustaining plant range shifts. It remains elusive whether the organization of interactions with seed dispersers is reconfigured along the expansion landscape template and, if so, whether its effects accelerate or slow colonization. Here we analyse plant-frugivore interactions in a scenario of rapid population expansion of a Mediterranean juniper. We combined network analyses with field surveys, sampling interactions between individual plants and frugivores by DNA-barcoding and phototrapping over two seasons. We assess the role of intrinsic and extrinsic intraspecific variability in shaping interactions and we estimate the individual plant contributions to the seed rain. The whole interaction network was highly structured, with a distinct set of modules including individual plants and frugivore species arranged concordantly along the expansion gradient. The modular configuration was partially shaped by individual neighbourhood context (density and fecundity) and phenotypic traits (cone size). Interaction reconfiguration resulted in a higher and more uneven propagule contribution, with most effective dispersers having a prominent role at the colonization front stand, where a distinct subset of early arriving plants dominated the seed rain. Our study offers new insights into the key role of mutualistic interactions in colonization scenarios by promoting fast plant expansion processes.

Colonization-competition dynamics of basal species shape food web complexity in island metacommunities

Exploring how food web complexity emerges and evolves in island ecosystems remains a major challenge in ecology. Food webs assembled from multiple islands are commonly recognized as highly complex trophic networks that are dynamic in both space and time. In the context of global climate change, it remains unclear whether food web complexity will decrease in a monotonic fashion when undergoing habitat destruction (e.g., the inundation of islands due to sea-level rise). Here, we develop a simple yet comprehensive patch-dynamic framework for complex food web metacommunities subject to the competition-colonization tradeoff between basal species. We found that oscillations in food web topological complexity (characterized by species diversity, mean food chain length and the degree of omnivory) emerge along the habitat destruction gradient. This outcome is robust to changing parameters or relaxing the assumption of a strict competitive hierarchy. Having oscillations in food web complexity indicates that small habitat changes could have disproportionate negative effects on species diversity, thus the success of conservation actions should be evaluated not only on changes in biodiversity, but also on system robustness to habitat alteration. Overall, this study provides a parsimonious mechanistic explanation for the emergence of food web complexity in island ecosystems, further enriching our understanding of metacommunity assembly.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00167-0.

Shortcomings of reusing species interaction networks created by different sets of researchers

Given the requisite cost associated with observing species interactions, ecologists often reuse species interaction networks created by different sets of researchers to test their hypotheses regarding how ecological processes drive network topology. Yet, topological properties identified across these networks may not be sufficiently attributable to ecological processes alone as often assumed. Instead, much of the totality of topological differences between networks-topological heterogeneity-could be due to variations in research designs and approaches that different researchers use to create each species interaction network. To evaluate the degree to which this topological heterogeneity is present in available ecological networks, we first compared the amount of topological heterogeneity across 723 species interaction networks created by different sets of researchers with the amount quantified from non-ecological networks known to be constructed following more consistent approaches. Then, to further test whether the topological heterogeneity was due to differences in study designs, and not only to inherent variation within ecological networks, we compared the amount of topological heterogeneity between species interaction networks created by the same sets of researchers (i.e., networks from the same publication) with the amount quantified between networks that were each from a unique publication source. We found that species interaction networks are highly topologically heterogeneous: while species interaction networks from the same publication are much more topologically similar to each other than interaction networks that are from a unique publication, they still show at least twice as much heterogeneity as any category of non-ecological networks that we tested. Altogether, our findings suggest that extra care is necessary to effectively analyze species interaction networks created by different researchers, perhaps by controlling for the publication source of each network.

Intraspecific variation in species interactions promotes the feasibility of mutualistic assemblages

Patterns of resource use observed at the species level emerge from the way individuals exploit the range of available resources. Hence, accounting for interindividual differences in resource use, such as pollinator use by plants, is essential to advance our understanding of community assembly and persistence. By using finely resolved data on plant-pollinator interactions, we evaluated how interindividual plant variation in pollinator use scales up to affect community structure and dynamics. All co-occurring plant species comprised specialists interacting with proper subsets of pollinators that visited generalists, and differences in interaction patterns were driven by among-individual trait variation. Furthermore, the nested structure and feasibility of plant-pollinator communities were maximised at higher levels of interindividual plant variation in traits and pollinator use. Our study sheds light on how pervasive properties of community structure arise from individual-level processes and contributes to elucidate the importance of preserving intraspecific variation in traits and resource use within populations.

Composition, structure and robustness of Lichen guilds

Symbiosis is a major engine of evolutionary innovation underlying many extant complex organisms. Lichens are a paradigmatic example that offers a unique perspective on the role of symbiosis in ecological success and evolutionary diversification. Lichen studies have produced a wealth of information regarding the importance of symbiosis, but they frequently focus on a few species, limiting our understanding of large-scale phenomena such as guilds. Guilds are groupings of lichens that assist each other's proliferation and are intimately linked by a shared set of photobionts, constituting an extensive network of relationships. To characterize the network of lichen symbionts, we used a large data set ([Formula: see text] publications) of natural photobiont-mycobiont associations. The entire lichen network was found to be modular, but this organization does not directly match taxonomic information in the data set, prompting a reconsideration of lichen guild structure and composition. The multiscale nature of this network reveals that the major lichen guilds are better represented as clusters with several substructures rather than as monolithic communities. Heterogeneous guild structure fosters robustness, with keystone species functioning as bridges between guilds and whose extinction would endanger global stability.

The Resilience of Plant-Pollinator Networks

There is growing awareness of pollinator declines worldwide. Conservation efforts have mainly focused on finding the direct causes, while paying less attention to building a systemic understanding of the fragility of these communities of pollinators. To fill this gap, we need operational measures of network resilience that integrate two different approaches in theoretical ecology. First, we should consider the range of conditions compatible with the stable coexistence of all of the species in a community. Second, we should address the rate and shape of network collapse once this safe operational space is exited. In this review, we describe this integrative approach and consider several mechanisms that may enhance the resilience of pollinator communities, chiefly rewiring the network of interactions, increasing heterogeneity, allowing variance, and enhancing coevolution. The most pressing need is to develop ways to reduce the gap between these theoretical recommendations and practical applications. This perspective shifts the emphasis from traditional approaches focusing on the equilibrium states to strategies that allow pollination networks to cope with global environmental change.

Book Review: On ecological networks and biological invasions

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Hidden effects of habitat restoration on the persistence of pollination networks

Past and recent studies have focused on the effects of global change drivers such as species invasions on species extinction. However, as we enter the United Nations Decade of Ecosystem Restoration the aim must switch to understanding how invasive-species management affects the persistence of the remaining species in a community. Focusing on plant-pollinator interactions, we test how species persistence is affected by restoration via the removal of invasive plant species. Restoration had a clear positive effect on plant persistence, whereas there was no difference between across treatments for pollinator persistence in the early season, but a clear effect in late season, with higher persistence in unrestored sites. Network structure affected only pollinator persistence, while centrality had a strong positive effect on both plants and pollinators. Our results suggest a hidden effect of invasive plants-although they may compete with native plant species, invasive plants may provide important resources for pollinators, at least in the short term.

Mutualist- and antagonist-mediated selection contribute to trait diversification of flowers

Flowers are generally short-lived, and they all face a multidimensional challenge because they have to attract mutualists, compel them to vector pollen with minimal investment in rewards, and repel floral enemies during this short time window. Their displays are under complex selection, either consistent or conflicting, to maximize reproductive fitness under heterogeneous environments. The phenological or morphological mismatches between flowers and visitors will influence interspecific competition, resource access, mating success and, ultimately, population and community dynamics. To better understand the effects of the plant visitors on floral traits, it is necessary to determine the functional significance of specific floral traits for the visitors; how plants respond to both mutualists and antagonists through adaptive changes; and to evaluate the net fitness effects of biological mutualisms and antagonism on plants. In this review, we bring together insights from fields as diverse as floral biology, insect behavioral responses, and evolutionary biology to explain the processes and patterns of floral diversity evolution. Then, we discuss the ecological significance of plant responses to mutualists and antagonists from a community perspective, and propose a set of research questions that can guide the research field to integrate studies of plant defense and reproduction.

Extinction of biotic interactions due to habitat loss could accelerate the current biodiversity crisis

Habitat loss disrupts species interactions through local extinctions, potentially orphaning species that depend on interacting partners, via mutualisms or commensalisms, and increasing secondary extinction risk. Orphaned species may become functionally or secondarily extinct, increasing the severity of the current biodiversity crisis. While habitat destruction is a major cause of biodiversity loss, the number of secondary extinctions is largely unknown. We investigate the relationship between habitat loss, orphaned species, and bipartite network properties. Using a real seed dispersal network, we simulate habitat loss to estimate the rate at which species are orphaned. To be able to draw general conclusions, we also simulate habitat loss in synthetic networks to quantify how changes in network properties affect orphan rates across broader parameter space. Both real and synthetic network simulations show that even small amounts of habitat loss can cause up to 10% of species to be orphaned. More area loss, less connected networks, and a greater disparity in the species richness of the network's trophic levels generally result in more orphaned species. As habitat is lost to land-use conversion and climate change, more orphaned species increase the loss of community-level and ecosystem functions. However, the potential severity of repercussions ranges from minimal (no species orphaned) to catastrophic (up to 60% of species within a network orphaned). Severity of repercussions also depends on how much the interaction richness and intactness of the community affects the degree of redundancy within networks. Orphaned species could add substantially to the loss of ecosystem function and secondary extinction worldwide.

Collapse of terrestrial mammal food webs since the Late Pleistocene

Food webs influence ecosystem diversity and functioning. Contemporary defaunation has reduced food web complexity, but simplification caused by past defaunation is difficult to reconstruct given the sparse paleorecord of predator-prey interactions. We identified changes to terrestrial mammal food webs globally over the past ~130,000 years using extinct and extant mammal traits, geographic ranges, observed predator-prey interactions, and deep learning models. Food webs underwent steep regional declines in complexity through loss of food web links after the arrival and expansion of human populations. We estimate that defaunation has caused a 53% decline in food web links globally. Although extinctions explain much of this effect, range losses for extant species degraded food webs to a similar extent, highlighting the potential for food web restoration via extant species recovery.

Emergent properties of species-habitat networks in an insular forest landscape

Deforestation and fragmentation are pervasive drivers of biodiversity loss, but how they scale up to entire landscapes remains poorly understood. Here, we apply species-habitat networks based on species co-occurrences to test the effects of insular fragmentation on multiple taxa-medium-large mammals, small nonvolant mammals, lizards, understory birds, frogs, dung beetles, orchid bees, and trees-across 22 forest islands and three continuous forest sites within a river-damming quasi-experimental landscape in Central Amazonia. Widespread, nonrandom local species extinctions were translated into highly nested networks of low connectance and modularity. Networks' robustness considering the sequential removal of large-to-small sites was generally low; between 5% (dung beetles) and 50% (orchid bees) of species persisted when retaining only <10 ha of islands. In turn, larger sites and body size were the main attributes structuring the networks. Our results raise the prospects that insular forest fragmentation results in simplified species-habitat networks, with distinct taxa persistence to habitat loss.

A network simplification approach to ease topological studies about the food-web architecture

Food webs studies are intrinsically complex and time-consuming. Network data about trophic interaction across different large locations and ecosystems are scarce in comparison with general ecological data, especially if we consider terrestrial habitats. Here we present a complex network strategy to ease the gathering of the information by simplifying the collection of data with a taxonomic key. We test how well the topology of three different food webs retain their structure at the resolution of the nodes across distinct levels of simplification, and we estimate how community detection could be impacted by this strategy. The first level of simplification retains most of the general topological indices; betweenness and trophic levels seem to be consistent and robust even at the higher levels of simplification. This result suggests that generalisation and standardisation, as a good practice in food webs science, could benefit the community, both increasing the amount of open data available and the comparison among them, thus providing support especially for scientists that are new in this field and for exploratory analysis.

Reduced evolutionary potential of a frugivorous bird species in fragmented forests

Morphological attributes are important in determining the success of ecological interactions, such as the interactions between fleshy fruited plants and their seed dispersers. Morphological traits can present high levels of intraspecific variation both within and across populations. Such variation will not only mediate which interactions can be established locally but also the potential for populations to respond to perturbations and selective pressure. Here, we investigated patterns of morphological variation (body weight and beaks’ traits) among different populations of blue manakin (Chiroxiphia caudata), in the highly fragmented Atlantic Forest, Brazil, both in terms of mean trait values – that might mediate interactions locally – and in their habitat-level variation which influences their evolutionary potential. Using metrics of evolutionary potential derived from quantitative genetics theory, we hypothesized that ecological stress would lead to a decline in the overall evolutionary potential in manakin populations. We found that populations differ slightly in their mean morphological attributes, with the exception of a population that occurs in temperate Araucaria forests. Nevertheless, we found a striking difference in the evolutionary potential of populations from different vegetation types. Specifically, populations that occur in ecological stress areas, Araucaria forests, and forest fragments immersed in savanna presented a smaller overall and conditional evolvability, suggesting their lower ability to respond in the direction of selection. This pattern might have important implications for the role of this species as seed disperser, as populations under stress may lack morphological variation (and covariation) that can be important to allow a given population to disperse seeds of multiple types of fruits. Moreover, a smaller evolvability might impact the potential of these populations to persist and perform their ecosystem services in face of environmental changes.

Local and collective transitions in sparsely-interacting ecological communities

Interactions in natural communities can be highly heterogeneous, with any given species interacting appreciably with only some of the others, a situation commonly represented by sparse interaction networks. We study the consequences of sparse competitive interactions, in a theoretical model of a community assembled from a species pool. We find that communities can be in a number of different regimes, depending on the interaction strength. When interactions are strong, the network of coexisting species breaks up into small subgraphs, while for weaker interactions these graphs are larger and more complex, eventually encompassing all species. This process is driven by the emergence of new allowed subgraphs as interaction strength decreases, leading to sharp changes in diversity and other community properties, and at weaker interactions to two distinct collective transitions: a percolation transition, and a transition between having a unique equilibrium and having multiple alternative equilibria. Understanding community structure is thus made up of two parts: first, finding which subgraphs are allowed at a given interaction strength, and secondly, a discrete problem of matching these structures over the entire community. In a shift from the focus of many previous theories, these different regimes can be traversed by modifying the interaction strength alone, without need for heterogeneity in either interaction strengths or the number of competitors per species.

Island and Mountain Ecosystems as Testbeds for Biological Control in the Anthropocene

For centuries, islands and mountains have incited the interest of naturalists, evolutionary biologists and ecologists. Islands have been the cradle for biogeography and speciation theories, while mountain ranges have informed how population adaptation to thermal floors shapes the distribution of species globally. Islands of varying size and mountains’ altitudinal ranges constitute unique “natural laboratories” where one can investigate the effects of species loss or global warming on ecosystem service delivery. Although invertebrate pollination or seed dispersal processes are steadily being examined, biological control research is lagging. While observations of a wider niche breadth among insect pollinators in small (i.e., species-poor) islands or at high (i.e., colder) altitudes likely also hold for biological control agents, such remains to be examined. In this Perspective piece, we draw on published datasets to show that island size alone does not explain biological control outcomes. Instead, one needs to account for species’ functional traits, habitat heterogeneity, host community make-up, phenology, site history or even anthropogenic forces. Meanwhile, data from mountain ranges show how parasitism rates of Noctuid moths and Tephritid fruit flies exhibit species- and context-dependent shifts with altitude. Nevertheless, future empirical work in mountain settings could clarify the thermal niche space of individual natural enemy taxa and overall thermal resilience of biological control. We further discuss how global databases can be screened, while ecological theories can be tested, and simulation models defined based upon observational or manipulative assays in either system. Doing so can yield unprecedented insights into the fate of biological control in the Anthropocene and inform ways to reinforce this vital ecosystem service under global environmental change scenarios.

Ehrlich and Raven escape and radiate coevolution hypothesis at different levels of organization: Past and future perspectives

The classic paper by Ehrlich and Raven on coevolution will soon be 60 years old. Although they were not the first to develop the idea of coevolution, their thought-provoking paper certainly popularized this idea and inspired several generations of scientists interested in coevolution. Here, we describe some of their main contributions, quantitatively measure the impact of their seminal paper on different fields of research, and discuss how ideas related to their original paper might push the study of coevolution forward. To guide our discussion, we explore their original hypothesis into three research fields that are associated with distinct scales/levels of organization: (1) the genetic mechanisms underlying coevolutionary interactions; (2) the potential association between coevolutionary diversification and the organization of ecological networks; and (3) the micro- and macroevolutionary mechanisms and expected patterns under their hypothesis. By doing so, we discuss potentially overlooked aspects and future directions for the study of coevolutionary dynamics and diversification.